A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

The essays in this book discuss human behavior and the institutions of capitalism. The essays are non-technical and are written so as to be accessible to students of all disciplines and to all other persons interested in capitalism and in economic behavior. They often present unconventional views of the topics they discuss. Those containing unconventional views discuss self-interested behavior, selfish gene theory, the meaning and social function of private ownership, the externality problem, the nature of the firm and the (...) rise of capitalism. The essays are not meant to be a textbook, but they offer a useful supplementary reading source for courses in business, economics and law that deal with human behavior in the marketplace and with capitalism, ownership, markets and firms. (shrink)

Radically new or unexpected findings in a science demand an openness to new concepts and styles of explanation. The time is more than ripe for asking ourselves what we have learned from the research program of comparative genomics. Where not long ago the human genome was expected to reveal a close association of complexity with the quantitative expansion of the roster of unique genes, more recent findings, especially in relation to comparisons between human and chimp, have raised the bracing possibility (...) that when it comes to complexity, it may be that `less is more'. But `less is more' is not the only observation or inference that follows from the data. The idea of `progressive detachment' will be introduced and set forth as the most perspicuous conceptual resource for unifying and interpreting the overall findings from comparative genomics to date. (shrink)

Vaccinia virus, the world's oldest vaccine, was used originally for the eradication of smallpox. It is now being genetically engineered to create new live vaccines for use against other infectious agents of medical and veterinary importance. Genes coding for antigens of several pathogens have been linked to vaccinia virus transcriptional regulatory signals and inserted into the vaccinia virus genome. The resultant recombinant viruses are infectious, express the foreign gene, stimulate specific immune responses in vaccinated animals and can protect against (...) disease caused by the corresponding pathogen. (shrink)

Abstract: Many believe that, in addition to cognitive capacities, autonomous robots need something similar to affect. As in humans, affect, including specific emotions, would filter robot experience based on a set of goals, values, and interests. This narrows behavioral options and avoids combinatorial explosion or regress problems that challenge purely cognitive assessments in a continuously changing experiential field. Adding human-like affect to robots is not straightforward, however. Affect in organisms is an aspect of evolved biological systems, from the taxes of (...) single-cell organisms to the instincts, drives, feelings, moods, and emotions that focus human behavior through the mediation of hormones, pheromones, neurotransmitters, the autonomic nervous system, and key brain structures. We argue that human intelligence is intimately linked to biological affective systems and to the unique repertoire of potential behaviors, sometimes conflicting, they facilitate. Artificial affect is affect in name only and without genes and biological bodies, autonomous robots will lack the goals, interests, and value systems associated with human intelligence. We will take advantage of their general intelligence and expertise, but robots will not enter our intellectual world or apply for legal status in the community. -/- . (shrink)

The concept of the gene has been the central organizing theme of 20th century biology. Biology has become increasingly influential both for philosophers seeking a naturalized basis for epistemology, ethics, and the understanding of the mind, as well as for the human sciences generally. The central task of this work is to get the story right about genes and in so doing provide a critical and enabling resourse for use in the further pursuit of human self-understanding. ;The work begins (...) with a wide-ranging historical reconstruction and conceptual analysis of the meaning of "the gene" that results in defining and distinguishing two different "genes". Each of these can be seen as an heir to one of the two major historical trends in explaining the source of biological order---preformationism and epigenesis. The preformationist gene predicts phenotypes but only on an instrumental basis where immediate medical and/or economic benefits can be had. The gene of epigenesis , by contrast, is a developmental resource that provides templates for RNA and protein synthesis but has in itself no determinate relationship to organismal phenotypes. The seemingly prevalent idea that genes constitute information for traits is based, I argue, upon an unwarranted conflation of these two senses which is in effect held together by rhetorical glue. Beyond this historical, conceptual, and rhetorical inquiry the bulk of the dissertation then concerns itself with an empirically up-to-date analysis of the cell and molecular basis of biological order and of the pathological loss of same. In each of these chapters I structure my analysis with the idea in mind that the "conflated" view can be held empirically accountable. Major touchpoints in this work include the ideas of I. Kant, J. Blumenbach, K. E. von Baer, J. Muller, R. Virchow, W. Johannsen, R. Falk, J. Sapp, E. Schrodinger, M. Delbruick, G. Gamow, R. Doyle, L. Kay, S. Kauffman, E. Jablonka, J. Rothman, K. Yamamoto, P. Rous, H. Temin, J. M. Bishop, H. Harris, E. Stanbridge, D. L. Smithers, B. Vogelstein, E. Farber and H. Rubin. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology (...) in order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

If the question ``What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to (...) the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about ``cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why ``genes'' should be of any special interst anyway. (shrink)

In her recent book Lindley Darden has endeavored to reclaim for philosophy an active role in the elaboration of good science. She has done this, not by holding up some set of rational standards derived from outside of scientific practice, but rather by delving into the history of science and coming out with a set of scientific strategies. Unconcerned about whether any particular strategy wasin fact employed in a given historical case her project depends upon two claims, first that these (...) strategiescould have been successfully deployed in the particular cases from which they were construed, and second and more importantly, that these strategies can be generalized beyond any particular context and be put to future use. It will be argued that Darden''s conception of the possible context independence of scientific strategies is based upon an overly cognitivist misconstrual. An alternative account of the relationship of context dependent and context independent aspects of scientific theory formation will be offered as well as its implications for philosophy. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a (...) framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Book review of Lenny Moss, What Genes Can’t Do. Cambridge, MA: MIT Press , 256 pp. -/- Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do. Moss argues that contemporary uses of the term ‘gene’ that denote an information bearing entity result from the conflation of two concepts (‘Gene-P’ and ‘Gene-D’).

Philosophy of Science, 73 (April 2006) pp. 247–257. 0031-8248/2006/7302-0007$10.00 Copyright 2006 by the Philosophy of Science Association. All rights reserved. 247 BOOK REVIEWS Lenny Moss, What Genes Can’t Do . Cambridge, MA: MIT Press (2004), 256 pp., $21.00 (paper). Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do . Moss argues that contemporary uses of the term ‘gene’ that denote an infor- mation bearing entity (...) result from the conflation of two concepts (‘Gene- P’ and ‘Gene-D’). These concepts arise out of distinct trajectories in the history of biology (preformation and epigenesis, respectively) but are glued together by the rhetoric of linguistic and textual metaphors (e.g., blueprints and programs). Gene-P picks out an instrumentalist use of ‘gene’ as phenotypic indicator or predictor, whereas Gene-D refers to DNA sequences as developmental template resources for RNA and pro- tein products that play variegated cellular roles in the production of many, distinct phenotypes. A number of critical responses to the distinction are now extant in the literature, but my aim is to answer a different question. Why should philosophers of science who have not read the book be interested in it (besides the fact that it is now available in paperback)? The answer is found at the level of methodology and is relevant to crit- icisms of Moss’s distinction. (shrink)

Traditional philosophical discussions of knowledge have focused on the epistemic status of full beliefs. In this book, Moss argues that in addition to full beliefs, credences can constitute knowledge. For instance, your .4 credence that it is raining outside can constitute knowledge, in just the same way that your full beliefs can. In addition, you can know that it might be raining, and that if it is raining then it is probably cloudy, where this knowledge is not knowledge of (...) propositions, but of probabilistic contents. -/- The notion of probabilistic content introduced in this book plays a central role not only in epistemology, but in the philosophy of mind and language as well. Just as tradition holds that you believe and assert propositions, you can believe and assert probabilistic contents. Accepting that we can believe, assert, and know probabilistic contents has significant consequences for many philosophical debates, including debates about the relationship between full belief and credence, the semantics of epistemic modals and conditionals, the contents of perceptual experience, peer disagreement, pragmatic encroachment, perceptual dogmatism, and transformative experience. In addition, accepting probabilistic knowledge can help us discredit negative evaluations of female speech, explain why merely statistical evidence is insufficient for legal proof, and identify epistemic norms violated by acts of racial profiling. Hence the central theses of this book not only help us better understand the nature of our own mental states, but also help us better understand the nature of our responsibilities to each other. (shrink)

This paper develops a precise understanding of the thesis of moral encroachment, which states that the epistemic status of an opinion can depend on its moral features. In addition, I raise objections to existing accounts of moral encroachment. For instance, many accounts fail to give sufficient attention to moral encroachment on credences. Also, many accounts focus on moral features that fail to support standard analogies between pragmatic and moral encroachment. Throughout the paper, I discuss racial profiling as a case study, (...) arguing that moral encroachment can help us identify one respect in which racial profiling is epistemically problematic. (shrink)

Traditional procedures for rational updating fail when it comes to self-locating opinions, such as your credences about where you are and what time it is. This paper develops an updating procedure for rational agents with self-locating beliefs. In short, I argue that rational updating can be factored into two steps. The first step uses information you recall from your previous self to form a hypothetical credence distribution, and the second step changes this hypothetical distribution to reflect information you have genuinely (...) learned as time has passed. While the second step resembles traditional procedures of updating by conditionalization, the first is best understood by analogy to traditional models of how agents transmit self-locating opinions through ordinary interpersonal communication. (shrink)

This is a modern, annotated translation of antiquity's only extant commentary on Plato's moral and political dialogue Gorgias , in which the author defends ancient Greek philosophy and culture at a time when Christianity has almost replaced it. The first translation into any modern language of a central work in Platonic studies is accompanied by annotations which guide the reader in understanding the obscurities of the text, an introduction to the main issues raised by it, and a bibliography of the (...) modern literature. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific (...) organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

In March 1996, the General Accounting Office issued the report Scientific Research: Continued Vigilance Critical to Protecting Human Subjects. It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always clear (...) to clinicians. Controversy exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

This article provides an analysis of bioprinting personalised medical device technology and its ethical challenges to regulation and research ethics. I argue the inclusion of bioprinting applications within existing regulatory frameworks does not adequately address the technologies disruption to the traditionally siloed activities of research and treatment. Using the conceptual framework of liminality, I offer a meaningful way to engage with this technology and address some identified concerns with how it will be categorised and the appropriate recognition of its evidentiary (...) thresholds. I demonstrate these concerns through the exploration of limited conventional research methodologies tasked with the production of generalisable knowledge, specifically population-based evidence that is derived from Randomised Clinical Trials. I use Australian regulatory amendments introduced in 2021 as an example of current regulatory trajectories and highlight why I believe this approach to be insufficient. The significance of this argument will be to demonstrate the disruption of bioprinting applications to current approaches in medical policy, and how various jurisdictions are enacting regulation that is not fit for purpose. (shrink)

The social structures and thought patterns of the modern world are the fruits of the Enlightenment, which begins by eliminating final causal explanations in favour of purely material and efficient causes. The development and great technical success of Enlightenment procedures has, however, produced a cultural blindness about the good. Camus's novel shows us this cultural blindness through characters who themselves suffer from it; for modern man, it is almost a natural evil—we are born into it. Camus' hope must have been (...) that the vision of the characters' incapacity might help break us from the same incapacity. What the cured life looks like Camus does not say; in the world of our plague, it appears as either odd or mystery. (shrink)

Used by more than one million students around the world since its original publication, this introductory philosophy text makes accessible a wide range of philosophical issues closely related to everyday life. Emphasizing personal and immediate questions, the authors approach introductory philosophy through basic human questions rather than focusing on methodology or the history of thought. The text presents vital questions of contemporary interest in an overall framework of enduring concepts, interweaving coverage of various topics in art, history, and education. It (...) covers a variety of types of philosophy in depth, and both western and eastern perspectives are represented. Ideal for students who have no background in philosophy, Living Issues in Philosophy, 9/e simplifies technical language wherever possible; unfamiliar terms are clearly defined upon first appearance and in the end-of-chapter glossaries. Additional pedagogical features include exercises, chapter summaries, and annotated bibliographies at the end of every chapter. The text also features photo biographies of major philosophers and short excerpts from philosophical classics. (shrink)

Book Review: What Genes Can’t Do By Lenny Moss .

The American University Publications In From its inception Philosophy has continued the direction stated in the sub-title of the initial volume that of probing new directions in philosophy. As the series has developed these probings of new directions have taken the two fold direction of exploring the relationships between the disparate traditions of twentieth century philosophy and with developing new insights into the foundations of some enduring philosophic problems. This present volume continues both of these directions. The interaction between twentieth-century (...) Anglo-Saxon and Continental philosophy which was an implicit theme of our first and third volumes and the explicit subject of our second volume is here continued in a series of studies on major figures and topics in each tradition. In the context of these interpretative studies, Professor Durfee returns again and again to the question of the relationships between the will and the reason, and explores the conflicting goals of creativity and objectivity in formulating a philosophic position. In so doing he raises the issue as his title suggests - of the foundations of philosophy itself. He seriously challenges the belief common to both pheomenology and analytic philosophy that philosophizing can be a presuppositionless activity, objectively persued independent of the personal (and, perhaps, arbitrary) commitments of the philosopher. This issue, critical as it is to all forms of philosophy, is surely a worthy one for a series such as ours. (shrink)

The ethical and political dilemmas raised byInformation and Communication Technology (ICT)have only just begun to be understood. Theimpact of centralised data collection, masscommunication technologies or the centrality ofcomputer technology as a means of accessingimportant social institutions, all poseimportant ethical and political questions. As away of capturing some of these effects I willcharacterise them in terms of the type of powerand, more particularly, the ‘Power-over’ peoplethat they exercise. My choice of thisparticular nomenclature is that it allows us todescribe, firstly, how specific (...) technologiesoperate and second, exactly what sorts ofconstraints they impose on people. The reasonfor this focus has to do with a further aim ofthe essay, which is to intervene in aparticular type of debate that is often hadaround the appropriate use and scope oftheories of power that are employed in thinkingabout ICT, especially those theories associatedwith the work of Michel Foucault. There isconsiderable use of his work in computerethics, but my claim will be that despite theproductive uses of his work in the areas ofsurveillance, for instance, it does not exhaustthe larger potential of his work on power and,in part, `government.' I will argue that inorder to properly understand the politicalimpact of some aspects of ICT, especially thedigital divide, one needs an account of howpower operates that includes more traditionaltypes of power-over. To the extent that I willdeal with these concerns, the paper is both acontribution to debates about the nature andscope of Foucault's theory of power and to theissue of the effects of the digital divide. (shrink)

Much of the debate about identity in recent decades has been about personal identity, and specifically about personal identity over time, but identity generally, and the identity of things of other kinds, have also attracted attention. Various interrelated problems have been at the centre of discussion, but it is fair to say that recent work has focussed particularly on the following areas: the notion of a criterion of identity; the correct analysis of identity over time, and, in particular, the disagreement (...) between advocates of perdurance and advocates of endurance as analyses of identity over time; the notion of identity across possible worlds and the question of its relevance to the correct analysis of de re modal discourse; the notion of contingent identity; the question of whether the identity relation is, or is similar to, the composition relation; and the notion of vague identity. A radical position, advocated by Peter Geach, is that these debates, as usually conducted, are void for lack of a subject matter: the notion of absolute identity they presuppose has no application; there is only relative identity. Another increasingly popular view is the one advocated by Lewis: although the debates make sense they cannot genuinely be debates about identity, since there are no philosophical problems about identity. Identity is an utterly unproblematic notion. What there are, are genuine problems which can be stated using the language of identity. But since these can be restated without the language of identity they are not problems about identity. (For example, it is a puzzle, an aspect of the so-called “problem of personal identity”, whether the same person can have different bodies at different times. But this is just the puzzle whether a person can have different bodies at different times. So since it can be stated without the language of personal “identity”, it is not a problem about identity, but about personhood.) This article provides an overview of the topics indicated above, some assessment of the debates and suggestions for further reading. (shrink)

The three volumes that make up Noise in Nonlinear Dynamical Systems comprise a collection of specially written authoritative reviews on all aspects of the subject, representative of all the major practitioners in the field.